## User: stuart

stuart10
Reputation:
10
Status:
New User
Location:
Last seen:
1 month ago
Joined:
3 years, 8 months ago
Email:
s************@monash.edu

#### Posts by stuart

<prev • 7 results • page 1 of 1 • next >
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... Thank you Michael. However, I found that mcols(dds)$maxCooks was all NAs by default when n=2, so I added it with:  mcols(dds)$maxCooks <- apply(assays(dds)[["cooks"]],1,max)  I hope this is equivalent to the normal calculation. Best, Stuart ...
written 3 months ago by stuart10
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... Hi all, We have a 2-factor, 2 levels per factor experimental design with 2 replicates per covariate combination (so 8 samples total, n=2 per cell) that we are analysing using DESeq2. Normally DESeq2 generates a Cook's distance for each replicate within a cell (by "cell" I mean unique combination ...
written 3 months ago by stuart10 • updated 3 months ago by Michael Love25k
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... Ah, I see now, thanks for the clarification. Actually I just realised that mcols(dxrTEST1)\$description gives some of this information, but it's useful to know where and when VST is applied too. ...
written 16 months ago by stuart10
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... Hi Alejandro, Thanks a lot, that's really helpful. Just a related question on the results object, as I want to make sure I genuinely understand how the log2fold-change is calculated: if I set gene_1:exon1 to be upregulated ~10-fold specifically in mut=='A' and treat='trt' by inserting some higher ...
written 16 months ago by stuart10
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... Dear all, I have a multifactorial experimental design (3 mutants and 2 treatments) am trying to obtain the difference of differences for exon usage. I can obtain p-values but not the fold-change of expression that is attributable to the interaction between mutant and treatment. I hope this makes se ...
written 16 months ago by stuart10 • updated 16 months ago by Alejandro Reyes1.7k
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... Thank you very much, this was really helpful. The duplicated genes show an average ~ +0.8 logFC. This is less than +1.0 probably due to homeostatic mechanisms at play, which indicates that I should treat duplicated genes that are downregulated from the logFC +1.0 baseline with caution. Nonetheless ...
written 3.7 years ago by stuart10
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... Hello, I am analysing RNA-seq data to find differentially expressed genes between a wild-type (Ctl) and mutant (Mut). The mutant has a large DNA duplication encompassing several hundred genes, so they always come up as ~2x upregulated but this is not biologically interesting. Hence the H0 (null) fo ...
written 3.7 years ago by stuart10

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